* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
* Support providing a distance matrix for molecule embedding
* a bit of parameter checking
* allow fragmentation before embedding to be disabled
* fix a build problem on windows
change in response to review
* Fixes#2057
docs still need to be updated
* docs update
* Update getting started doc.
This still needs to have the doctests run and should probably be
proofread and tweaked
* some doc updates
* change in response to review
* Make sure EmbedMultipleConfs is deterministic for very large seeds and a seed of 0.
Fixing two distinct bugs:
- A randomSeed of 0 didn't use '0' as the seed even though the
documentation said that it should.
- Very large seeds could overflow the 'int' representation during
calculation of a new internal seed. This would make
EmbedMultipleConfs non-deterministic even though the user provided a
valid seed.
* Adding a C++ test for case pull request #1635.
* version 2 of ETKDG
* setting default and changing to unsigned int
* ETversion 2 only via EmbedParams available
* Some refactoring so that the DG functions that take the parameter object are the primaries.
This should allow new parameters to be added without having to modify the API
* test and wrapper changes to go along with that
* update cookbook to use etkdg
* Fix a bug in the python DistGeom tests.
* test new features
* add simple parameter objects for ETDG, ETKDG, and KDG
* Update conformation generation documentation to use the new parameter objects.
* initial version; no actual testing yet
* start on tests
* rename seed->randomSeed; add tests
* add support in java wrapper
* add support in python wrapper
* initial version; no actual testing yet
* start on tests
* rename seed->randomSeed; add tests
* add support in java wrapper
* add support in python wrapper
* yapf
* document the parameter object;
introduce pre-defined const objects for ETDG, ETKDG, and KDG
* this is why we write tests
* swig did not like the initialization in the header file
GraphMol/DistGeomHelpers/:
Support generating random initial coordinates of atoms as an alternative to embedding. This has so far only been tested on windows (all tests pass) and it needs to be optimized (particularly force field parameters).
Other changes here are primarily cosmetic code cleanups.
